In the good old tradition of making up armchair evolutionary psychology "explanations" (aka just so stories), here is my uneducated guess:
In the ancestral environment, abnormal behavior patterns (unusual body language or lack of proper feedback to body language, unusual vocalizations, poor motor coordination, anything "odd" in general) were symptoms of neurological disorders. Neurological disorders were typically caused by infectious diseases, because, well, infectious diseases were so common back then that pretty much any disorder was probably caused by them.
So, there is this odd-behaving ape. The apes that are not bothered by that and keep hanging around it or, gods forbid, mate with it, catch meningitis or some other nasty bug and die. The apes who are creeped the hell out of it avoid infection and get to pass their genes.
Fast forward a couple million years, to some odd-behaving dude. Chances are that he has no infectious disease. Maybe an autism spectrum condition, or poor socialization or socialization in a different culture, or whatnot. But your ape amygdalae don't know that. They just say to your cortex "odd behavior = mortal threat".
Perhaps you rationalize this visceral fear as justified adversion to risk of assault, but it may be actually an innate response evolved for something completely unrelated.
Then why is creepiness so gendered?
One of the lessons highlighted in the thread "Less Wrong NYC: Case Study of a Successful Rationalist Chapter" is Gender ratio matters.
There have recently been a number of articles addressing one social skills issue that might be affecting this, from the perspective of a geeky/sciencefiction community with similar attributes to LessWrong, and I want to link to these, not just so the people potentially causing problems get to read them, but also so everyone else knows the resource is there and has a name for the problem, which may facilitate wider discussion and make it easier for others to know when to point towards the resources those who would benefit by them.
However before I do, in the light of RedRobot's comment in the "Of Gender and Rationality" thread, I'd like to echo a sentiment from one of the articles, that people exhibiting this behaviour may be of any gender and may victimise upon any gender. And so, while it may be correlated with a particular gender, it is the behaviour that should be focused upon, and turning this thread into bashing of one gender (or defensiveness against perceived bashing) would be unhelpful.
Ok, disclaimers out of the way, here are the links:
Some of those raise deeper issues about rape culture and audience as enabler, but the TLDR summary is:
EDITED TO ADD:
Despite the way some of the links are framed as being addressed to creepers, this post is aimed at least as much at the community as a whole, intended to trigger a discussion on how the community should best go about handling such a problem once identified, with the TLDR being "set of restraints to place on someone who is burning the commons", rather that a complete description that guarantees that anyone who doesn't meet it isn't creepy. (Thank you to jsteinhardt for clearly verbalising the misinterpretation - for discussion see his reply to this post)